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DOE OSTI2024

FuseIM: Fusing Probabilistic Traversals for Influence Maximization on Exascale Systems

Probabilistic breadth-first traversals (BPTs) are used in many network science and graph machine learning applications. In this paper, we are motivated by the application of BPTs in stochastic diffusion-based graph problems such as influence maximization. These applications heavily rely on BPTs to implement a Monte-Carlo sampling step for their approximations. Given the large sampling complexity, stochasticity of the diffusion process, and the inherent irregularity in real-world graph topologies, efficiently parallelizing these BPTs remains significantly challenging. In this paper, we present a new algorithm to fuse massive number of concurrently executing BPTs with random starts on the input graph. Our algorithm is designed to fuse BPTs by combining separate traversals into a unified frontier on distributed multi-GPU systems. To show the general applicability of the fused BPT technique, we have incorporated it into two state-of-the-art influence maximization parallel implementations (gIM and Ripples). Our experiments on up to 4K nodes of the OLCF Frontier supercomputer (32,768 GPUs and 196K CPU cores) show strong scaling behavior, and that fused BPTs can improve the performance of these implementations up to 34x (for gIM) and ~360x (for Ripples).

Neff, Reece W.↗

DOE OSTI2025

Understanding Redox Organic Behavior in Deep Eutectic Solvents: Considerations for Molecular Design

Electrolytes based on deep eutectic solvents (DESs) coupled with redox active organic molecules have shown potential as a versatile and energy dense electrochemical energy storage system. However, progress in these systems has been held back by a lack of understanding of the irregular behavior displayed when redox active organic molecules are transitioned from other solvent systems. In this work, the hydrogen bonding characteristics of a series of redox organic molecules were investigated through infrared spectroscopy and molecular modeling. New understanding of these interactions was then used to explain their electrochemical behavior in a DES electrolyte. A model was used to predict the behavior of new derivatives towards the design of an optimized redox organic-DES system. Hydrogen bonding between the redox molecules and the solvent was found to significantly shift the potential of a redox reaction more positive when a hydrogen bond forms at the redox active site. It was predicted that functionalizing a molecule with electron withdrawing groups to lower the electron density of the redox active functional group lowers the strength of the hydrogen bond and thus alleviates the undesirable potential shift. This hypothesis was demonstrated by the addition of nitro groups to fluorenones.

25 ENERGY STORAGE↗

DOE OSTI2022

A New Model for Simulating the Imbibition of a Wetting-Phase Fluid in a Matrix-Fracture Dual Connectivity System

The imbibition experiment is an effective approach for measuring petrophysical properties of porous media, with many such experiments performed over the past decade. Quite some empirical, analytical, and numerical models have been developed to simulate spontaneous imbibition of the wetting phase fluid into porous media, but limitations still exist. In previous studies, the imbibition process has been considered to give a piston-like displacement or the porous medium modeled as multiply-sized pores linked with bonds; both approaches fail to yield comprehensive results due to their neglect of the presence of irregular fractures or nonuniform flow paths through the matrix. By building a numerical model for simulating laboratory-scale experimental data, we performed imbibition tests on several fractured Barnett Shale samples having fractures either parallel ( P ) or transverse ( T ) to the bedding plane and used MATLAB to build a new numerical model by combining the imbibition process in fractures and the matrix using concepts from percolation theory. The experimental data show that the rocks with P -direction fractures have a more steady increase of imbibition rates than the case of T -direction one. As the shale matrix with low pore connectivity hampers the upward water movement, the imbibition rate of shales with T -direction fractures will decrease suddenly after the bottom layer in contact with water is saturated during the initial period. This wetting phase movement (WPM) model can simulate 3D porous media with 2D fractures. The rate of imbibition by fractured porous media is associated with physical parameters such as porosity and fracture distribution (e.g., the number and angle of fractures). Using Monte Carlo methods, we examined fracture parameters and predicted elapsed time and cumulative water imbibition, for the Barnett Shale samples. The results show that the rate of imbibed water mass is sensitive to the number of fractures directly connected to water source, and the connectivity between two neighboring grid cells is a key parameter for the wetting-front progression. The findings of this study can help to better understand the imbibition process with multiple influencing processes and factors in fractured-matrix rocks. Although the experiments, data simulation, and prediction results are based only on Barnett Shale samples, the model is readily applicable to imbibition tests of other fractured rocks to show the spatial and temporal behavior during a dynamic imbibition process that are not easily captured experimentally.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2020

Distributed Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper (DiBELLA) v1.0.0

We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers. While long sequences of DNA offer enormous advantages for biological analysis and insight, current long read sequencing instruments have high error rates and therefore require different approaches to analysis than their short read counterparts. Our work focuses on an efficient distributed-memory parallelization of an accurate single-node algorithm for overlapping and aligning long reads. We achieve scalability of this irregular algorithm by addressing the competing issues of increasing parallelism, minimizing communication, constraining the memory footprint, and ensuring good load balance. The resulting application, DiBELLA, is the first distributed memory overlapper and aligner specifically designed for long reads and parallel scalability.

Ellis, Marquita↗

DOE OSTI2022

A Hybrid Bulk Algorithm to Predict Turbulent Fluxes over Dry and Wet Bare Soils

Measurements made in the Columbia River basin (Oregon) in an area of irregular terrain during the second Wind Forecast Improvement Project (WFIP2) field campaign are used to develop an optimized hybrid bulk algorithm to predict the surface turbulent fluxes from readily measured or modeled quantities over dry and wet bare or lightly vegetated soil surfaces. The hybrid (synthetic) algorithm combines (i) an aerodynamic method for turbulent flow, which is based on the transfer coefficients (drag coefficient and Stanton number), roughness lengths, and Monin–Obukhov similarity; and (ii) a modified Priestley–Taylor (P-T) algorithm with physically based ecophysiological constraints, which is essentially based on the surface energy budget (SEB) equation. Soil heat flux in the latter case was estimated from measurements of soil temperature and soil moisture. In the framework of the hybrid algorithm, bulk estimates of the momentum flux and the sensible heat flux are derived from a traditional aerodynamic approach, whereas the latent heat flux (or moisture flux) is evaluated from a modified P-T model. Direct measurements of the surface fluxes (turbulent and radiative) and other ancillary atmospheric/soil parameters made during WFIP2 for different soil conditions (dry and wet) are used to optimize and tune the hybrid bulk algorithm. The bulk flux estimates are validated against the measured eddy-covariance fluxes. We also discuss the SEB closure over dry and wet surfaces at various time scales based on the modeled and measured fluxes. Although this bulk flux algorithm is optimized for the data collected during the WFIP2, a hybrid approach can be used for similar flux-tower sites and field campaigns.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Relationships between Immersion Freezing and Crystal Habit for Arctic Mixed-Phase Clouds—A Numerical Study

Abstract The number concentration of ice particles in Arctic mixed-phase clouds is a major controlling factor of cloud lifetime. The relationships between ice nucleation mode and ice crystal habit development are not yet constrained by observations. This study uses a habit-predicting microphysical scheme within a 3D large-eddy simulation model to evaluate the relationship between immersion freezing and ice habit in a simulated Arctic mixed-phase cloud case. Three immersion freezing parameterizations are considered: a volume-dependent freezing scheme (VF), a parameterization limited to activated droplets (C-AC), and a parameterization limited to coarse aerosol particles (C-CM). Both C-AC and C-CM are based on classical nucleation theory. The freezing rate with VF is found to be greater in downdraft regions than in updraft regions due to the downdraft having a higher number concentration of large droplets. The C-AC cases show active freezing of small droplets near cloud top, whereas in the C-CM cases, mainly the 8–32- μ m-sized droplets freeze in updraft regions near the cloud base. Because the initial crystal size is assumed to affect the axis ratio of hexagonal plates, the VF cases produce crystals with larger axis ratios, resulting in smaller mode radii than the C-AC cases. In all cases, irregular polycrystals dominate near cloud top and a band-like structure develops within the cloud, which qualitatively agrees with previous observations. In the VF and C-CM cases, unactivated large droplets arising from coarse-mode aerosol particles contributed significantly to the freezing rate, producing an important influence on crystal habit.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Multi-scale Analysis of Surface Heterogeneity Induced Convection on Isentropic Coordinates

This research uses semi-idealized simulations to investigate multi-scale processes induced by the heterogeneity of soil moisture observed during the 2016 Holistic Interactions of Shallow Clouds, Aerosols, and Land-Ecosystems (HI-SCALE) field campaign. The semi-idealized simulations have realistic land heterogeneity, but large-scale winds are removed. Analysis on isentropic coordinates enables the tracking of circulation that transports energy vertically and facilitates the identification of the primary convective processes induced by realistic land heterogeneity. The isentropes associated with upward motion are found to connect the ground characterized by high latent heat flux to cloud bases directly over the ground with high sensible heat flux, while isentropes associated with downward motion connect precipitation to the ground characterized by high sensible heat fluxes. The mixing of dry, warm parcels ascending from the ground with high sensible heat fluxes and moist parcels from high latent heat regions leads to cloud formation. This new mechanism explains how soil moisture heterogeneity provides the key ingredients such as buoyancy and moisture for shallow cloud formation. We also found that the sub-mesoscale dominates upward energy transport in the boundary layer, while mesoscale circulations contribute to vertical energy transport above the boundary layer. Our novel method better illustrates and elucidates the nature of land atmospheric interactions under irregular and realistic soil moisture patterns.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Near-Real-Time Forecast of Satellite-Based Soil Moisture Using Long Short-Term Memory with an Adaptive Data Integration Kernel

Nowcasts, or near-real-time (NRT) forecasts, of soil moisture based on the Soil Moisture Active and Passive (SMAP) mission could provide substantial value for a range of applications including hazards monitoring and agricultural planning. To provide such a NRT forecast with high fidelity, we enhanced a time series deep learning architecture, long short-term memory (LSTM), with a novel data integration (DI) kernel to assimilate the most recent SMAP observations as soon as they become available. The kernel is adaptive in that it can accommodate irregular observational schedules. Testing over the CONUS, this NRT forecast product showcases predictions with unprecedented accuracy when evaluated against subsequent SMAP retrievals. It showed smaller error than NRT forecasts reported in the literature, especially at longer forecast latency. The comparative advantage was due to LSTM’s structural improvements, as well as its ability to utilize more input variables and more training data. The DI-LSTM was compared to the original LSTM model that runs without data integration, referred to as the projection model here. We found that the DI procedure removed the autocorrelated effects of forcing errors and errors due to processes not represented in the inputs, for example, irrigation and floodplain/lake inundation, as well as mismatches due to unseen forcing conditions. The effects of this purely data-driven DI kernel are discussed for the first time in the geosciences. Furthermore, this work presents an upper-bound estimate for the random component of the SMAP retrieval error.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Laser-Induced Plasmas of Plutonium Dioxide in a Double-Walled Cell

Plutonium research has been stifled by the significant number of administrative controls and safety procedures, space and instrumentation limitations in radiological gloveboxes, and the potential for personnel and equipment contamination. To address the limited number of spectroscopic studies in Pu-bearing compounds in the current scientific literature, this work presents the use of double-walled cells (DWCs) in “clean” buildings/laboratories as an alternative to research in radiological gloveboxes. This study reports the first laser-induced breakdown spectroscopy (LIBS) experiments of a PuO 2 pellet contained within a DWC, where the formation of elemental (atomic and ionic) species as well as the evolution from elemental to molecular products (Pu x O y ) was measured. Raman spectroscopy was also used to characterize the surface of the ablated pellet and the particulates deposited on the window of the inner cell. The full width half-maximum of the T 2g band enabled us to obtain an estimate of the temperature at the pellet surface after the ablation pulse and the particulates based on the crystal lattice disorder. Particulates deposited on the window of the DWC during laser ablation were characterized using scanning electron microscopy, where molten irregular particulates and spheroids were observed. This exciting research conducted in a DWC describes our initial attempts to incorporate LIBS in the arsenal of spectroscopic tools for nuclear forensics applications.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2025

Confocal Raman Microscopy as a Probe of Material Deconstruction in Processed Low-Density Polyethylene Particles

Confocal Raman microscopy was applied to detect structural change within individual particles of low-density polyethylene (LDPE) following chemical and electrochemical processing steps that aimed to facilitate material decomposition. A high numerical aperture (NA) oil-immersion objective enabled depth-profiling through the near surface region (20 μm–40 μm) of irregularly shaped particles with an axial spatial resolution < 2 μm estimated from measurements of instrument detection efficiency profiles. Changes in vibrational bands sensitive to polyethylene crystallinity were evident following treatments and linked to the release of low molecular weight compounds present as additives and products of processing. Effects of processing were probed by monitoring the rise of Raman scattering intensity in vibrational modes associated with polyethylene chains in a zig-zag (trans) conformation near 1128 cm –1 , 1294 cm –1 , and 1418 cm –1 , signaling chain clustering and development of organized, crystalline-like assemblies. Pristine LDPE particles displayed a uniform structure across the near surface region, while particles treated initially with chemical extractant and then further processed displayed increasingly enhanced crystallinity up to the maximum depth probed (40 μm). As a step toward measurements on ensembles of particles, least squares modeling was adapted to derive pure component spectra reflecting crystallinity change within spectral datasets. The work demonstrates high spatial resolution Raman depth-profiling for the characterization of processed polymers using a high NA immersion objective to overcome the limitations of air-objectives often used for confocal Raman microscopy.

Wahiduzzaman, Md. [Department of Chemistry and Bio↗

DOE OSTI2021

EXAGRAPH: Graph and combinatorial methods for enabling exascale applications

Combinatorial algorithms in general and graph algorithms in particular play a critical enabling role in numerous scientific applications. However, the irregular memory access nature of these algorithms makes them one of the hardest algorithmic kernels to implement on parallel systems. With tens of billions of hardware threads and deep memory hierarchies, the exascale computing systems in particular pose extreme challenges in scaling graph algorithms. The codesign center on combinatorial algorithms, ExaGraph, was established to design and develop methods and techniques for efficient implementation of key combinatorial (graph) algorithms chosen from a diverse set of exascale applications. Algebraic and combinatorial methods have a complementary role in the advancement of computational science and engineering, including playing an enabling role on each other. In this paper, we survey the algorithmic and software development activities performed under the auspices of ExaGraph from both a combinatorial and an algebraic perspective. In particular, we detail our recent efforts in porting the algorithms to manycore accelerator (GPU) architectures. We also provide a brief survey of the applications that have benefited from the scalable implementations of different combinatorial algorithms to enable scientific discovery at scale. We believe that several applications will benefit from the algorithmic and software tools developed by the ExaGraph team.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Enhancing scalability of a matrix-free eigensolver for studying many-body localization

We propose several techniques to enhance the parallel scalability of a matrix-free eigensolver designed for studying many-body localization (MBL) of quantum spin chain models with nearest-neighbor interactions and on-site disorder. This type of problem is computationally challenging because the dimension of the associated Hamiltonian matrix grows exponentially with respect to the number of spins L, and we need to average over different realizations of the random disorder to obtain relevant statistical behavior. For each disorder realization, we need to compute eigenvalues from different regions of the spectrum and their corresponding eigenvectors. In previous work, the interior eigenstates for a single eigenvalue problem are computed via the shift-and-invert Lanczos algorithm. Due to the extremely high memory footprint of the LU factorizations, this technique is not well suited for large L’s. For example, we need thousands of compute nodes on modern high performance computing infrastructures to go beyond L = 24. The matrix-free approach does not suffer from this memory bottleneck, however, its scalability is limited by a computation and communication load imbalance. To reduce this imbalance and to significantly enhance the scalability of the matrix-free eigensolver, we reorder the matrix and leverage the consistent space runtime, CSPACER. We also show its efficiency in managing irregular communication patterns at scale compared to optimized MPI non-blocking two-sided and one-sided RMA implementation variants. This effort enables us to study MBL for spin chains with a larger number of spins. The efficiency and effectiveness of the proposed algorithm is demonstrated by computing eigenstates on a massively parallel many-core high performance computer.

METIS↗

DOE OSTI2024

PaRSEC: Scalability, flexibility, and hybrid architecture support for task-based applications in ECP

This paper highlights the most significant enhancements made to PaRSEC, a scalable task-based runtime system designed for hybrid machines, during the Exascale Computing Project (ECP). The enhancements focus on expanding the capabilities of PaRSEC to address the evolving landscape of parallel computing. Notable achievements include the integration of support for three major types of accelerators (NVIDIA, AMD, and Intel GPUs), the refinement and increased flexibility of the communication subsystem, and the introduction of new programming interfaces tailored for irregular applications. Additionally, the project resulted in the development of powerful debugging and performance analysis tools aimed at assisting users in understanding and optimizing their applications. We present a comprehensive demonstration of these advancements through a series of benchmarks and applications within ECP and beyond, thereby showcasing the enhanced capabilities of PaRSEC across the diverse architectures within the ECP, providing valuable insights into the runtime system’s adaptability and performance across varied computing environments.

Bouteiller, Aurelien↗

DOE OSTI2026

Accurate measurement of porosity size and morphology in aluminium alloy laser welds

Conventional two-dimensional optical microscopy is the most common tool for capturing and quantifying keyhole collapse porosity and other defects formed during the laser welding of aluminium alloys. This approach is of limited utility since only a single longitudinal or transverse metallographic cross-section, comprising only a small fraction of the overall weld volume, can be extracted or analysed at a time. X-ray computed tomography tools, on the other hand, enable three-dimensional visualisation and analysis of porosity and defects to be made across the full weld volume. When comparing these two measurement techniques, two-dimensional microscopy tools significantly underestimated the fraction of defects present within the weld at levels between 50% and 80%. Three-dimensional x-ray computed tomography tools also provide a means for accurately characterising the location, size and morphology of irregularly shaped defects. By categorising the defect shapes using a Zingg's shape analysis, in which the distribution of defect morphologies could be quantified as disk, rod and spherical shapes, a transition in defect morphology moving from stationary beam to oscillating beam welds was detected and quantified.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Thermobifida fusca Cel6B moves bidirectionally while processively degrading cellulose

Abstract Background Cellulose, an abundant biopolymer, has great potential to be utilized as a renewable fuel feedstock through its enzymatic degradation into soluble sugars followed by sugar fermentation into liquid biofuels. However, crystalline cellulose is highly resistant to hydrolysis, thus industrial-scale production of cellulosic biofuels has been cost-prohibitive to date. Mechanistic studies of enzymes that break down cellulose, called cellulases, are necessary to improve and adapt such biocatalysts for implementation in biofuel production processes. Thermobifida fusca Cel6B ( Tf Cel6B) is a promising candidate for industrial use due to its thermostability and insensitivity to pH changes. However, mechanistic studies probing Tf Cel6B hydrolytic activity have been limited to ensemble-scale measurements. Results We utilized optical tweezers to perform single-molecule, nanometer-scale measurements of enzyme displacement during cellulose hydrolysis by Tf Cel6B. Records featured forward motility on the order of 0.17 nm s −1 interrupted by backward motions and long pauses. Processive run lengths were on the order of 5 nm in both forward and backward directions. Motility records also showed rapid bidirectional displacements greater than 5 nm. Single-enzyme velocity and bulk ensemble activity were assayed on multiple crystalline cellulose allomorphs revealing that the degree of crystallinity and hydrogen bonding have disparate effects on the single-molecule level compared to the bulk scale. Additionally, we isolated and monitored the catalytic domain of Tf Cel6B and observed a reduction in velocity compared to the full-length enzyme that includes the carbohydrate-binding module. Applied force has little impact on enzyme velocity yet it readily facilitates dissociation from cellulose. Preliminary measurements at elevated temperatures indicated enzyme velocity strongly increases with temperature. Conclusions The unexpected motility patterns of Tf Cel6B are likely due to previously unknown mechanisms of processive cellulase motility implicating irregularities in cellulose substrate ultrastructure. While Tf Cel6B is processive, it has low motility at room temperature. Factors that most dramatically impact enzyme velocity are temperature and the presence of its native carbohydrate-binding module and linker. In contrast, substrate ultrastructure and applied force did not greatly impact velocity. These findings motivate further study of Tf Cel6B for its engineering and potential implementation in industrial processes.

Johnson, Madeline M. (ORCID:000000029518293X)↗

DOE OSTI2023

Covariate Dependent Sparse Functional Data Analysis

This study proposes a method to incorporate covariate information into sparse functional data analysis. The method aims at cases where each subject has a limited number of longitudinal measurements and is associated with static covariates. This research is motivated by several use cases in practice. One representative example is void swelling, a nuclear-specific material degradation mechanism. Void swelling is affected by many covariates, including alloy composition and irradiation type. How to accurately model the complicated joint effects of such covariates on the swelling process is the key to mitigating the effect of swelling and ensuring safe operation. Unlike most of the existing methods, the proposed method can handle high-dimensional covariates with the informative covariate identification procedure and sparse and irregularly spaced measurements, that is, does not require complete or dense observations. The main innovation of the proposed method is that we model the variation coming from covariates and the variation left conditioned on covariates, such that the functional principal component analysis and Gaussian process can be conducted in a unified manner. Further, we also propose a systematic approach to identify important covariates in the hypothesis testing context. The methodology is demonstrated on applications in nuclear engineering and healthcare and simulation studies.

42 ENGINEERING↗

DOE OSTI2020

Traversing large graphs on GPUs with unified memory

Due to the limited capacity of GPU memory, the majority of prior work on graph applications on GPUs has been restricted to graphs of modest sizes that fit in memory. Recent hardware and software advances make it possible to address much larger host memory transparently as a part of a feature known as unified virtual memory. While accessing host memory over an interconnect is understandably slower, the problem space has not been sufficiently explored in the context of a challenging workload with low computational intensity and an irregular data access pattern such as graph traversal. We analyse the performance of breadth first search (BFS) for several large graphs in the context of unified memory and identify the key factors that contribute to slowdowns. Next, we propose a lightweight offline graph reordering algorithm, HALO (Harmonic Locality Ordering), that can be used as a pre-processing step for static graphs. HALO yields speedups of 1.5x-1.9x over baseline in subsequent traversals. Our method specifically aims to cover large directed real world graphs in addition to undirected graphs whereas prior methods only account for the latter. Additionally, we demonstrate ties between the locality ordering problem and graph compression and show that prior methods from graph compression such as recursive graph bisection can be suitably adapted to this problem.

Gera, Prasun↗

DOE OSTI2022

HERO WEC V1.0 - WEC-Sim Detailed Simulation Runs and Summary Data

Data sets from simulation runs include 144 wave cases that were run based on the WEC-Sim model (https://mhkdr.openei.org/submissions/483). The 144 wave cases represent waves with the following wave height and wave period ranges: - Significant Wave Height: 0.25 - 4.0m in 0.25m increments - Wave Period: 5 - 13 sec in 1 sec increments Each run was simulated using a Pierson-Moskowitz irregular wave spectrum with a 200 second ramp time and a total simulation time of 2,200 seconds. Summary data set includes a spreadsheet and image files with matrices that are associated with data from simulation runs. All matrices cover the same significant wave height and wave periods from the sim runs, in the same increments. The following matrices are included: - Mechanical Power Input: Absorbed power calculated using linear input velocity at PTO (power take-off) multiplied by winch tension. - Mechanical Power Output: The hydraulic power calculated at the pump output prior to the pressure relief valve dump. - Feed Pressure: Average pressure at RO (reverse osmosis) input prior to pre-filters - RO Power Input: The hydraulic power calculated at the RO system inlet, accounts for flow loss due to pressure relief valve - Water Production: Average clean water flow at RO output

16 TIDAL AND WAVE POWER↗